


The One We Loved And Left Behind

by Signe (oxoniensis)



Category: Stargate Atlantis
Genre: Angst, Ensemble Cast, F/M, Gen, M/M, Minor Character Death, Sentient Atlantis
Language: English
Status: Completed
Published: 2006-04-19
Updated: 2006-04-19
Packaged: 2017-12-28 07:33:53
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 10,001
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/989414
Author URL: https://archiveofourown.org/users/oxoniensis/pseuds/Signe
Summary: <blockquote class="userstuff">
              <p>With hindsight, of course, it's obvious. The clues they missed, the warnings they ignored. Hindsight's a taunting bitch.</p>
            </blockquote>





	The One We Loved And Left Behind

**Author's Note:**

  * For [logovo](https://archiveofourown.org/users/logovo/gifts).



> Thanks to logovo for the prompt word (fever) that sparked the story. And a huge thank you to vegetariansushi, romanticalgirl, 2am_optimism and setissma for fantastic betas, writing me cylon!Zak fic and just being wonderful.

There are dead fish floating on the sea, scores of them, glassy-eyed and swollen-bellied. The water's hot and the fish stink. He looks down on them from the balcony, then lifts his hand to shade his eyes and stare across the horizon. It's the same in every direction he can see, an ugly sight.

John sits up suddenly, wide awake, and blinks into the dark. He can still picture the dead fish, feel the heat shimmering off the water, though he's clear-headed enough to know it was only a dream. He pads carefully across the room to the sink and pours himself a glass of water. He drinks it slowly and lets the dream fade.

It feels chilly in his room – he's not used to such cold nights anymore – so he turns up the thermostat, finds an extra blanket, and crawls back under the covers. Tomorrow he'll sneak some sleeping pills from the infirmary.

*

It starts, like bad things often do, so gradually that no one notices. Or, if they do notice that something is wrong, or even not so much _wrong_ as not quite right, they put it down to a system error, user error, tiredness, any of a hundred excuses that have been valid before and will be valid again.

But it isn't an error.

And with hindsight, of course, it's obvious. The clues they missed, the warnings they ignored. Hindsight's a taunting bitch.

*  
Elizabeth's is the first warning they can be certain of. Earlier clues may have been there, but they'll never be sure. They were too busy trying to survive – they need to remember that. They were caught up in the day-to-day business of living, so there wasn't time to look at everything, measure everything, listen to everything. They all tell each other that – that it wasn't their fault, they couldn't have seen the problem any earlier – but they all still blame themselves.

Elizabeth especially, now they understand how it started. Their Elizabeth, that is, even though, technically, it wasn't her that started it, and there was no way she could have guessed what might happen.

The other Elizabeth's warning is on tape though, so they can listen to it repeatedly and kick themselves for not seeing the meaning in it. Not hearing anything more than the ramblings of a ten thousand year old woman who could barely keep awake for a more than a few minutes at a time.

"It's too warm," she said. Beckett took her temperature and pronounced it normal – as normal as could be expected for a woman who'd been frozen for a thousand years, he added, and McKay interrupted to say she hadn't been frozen, per se, that metabolic stasis was something altogether different from simple freezing, and that carried on for a while – and no one thought anything of it. And then they were too excited about the possibility of finding the outposts with the stored ZPMs, and it was too late to listen to her anymore, even if they had understood the need, understood the warning in those three simple words.

*

They are in a different galaxy. That's the answer to so much. They can't expect things to be exactly the same here, for their old definitions of normal to apply. They can't expect to be sleeping well when the planet they are living on takes thirty hours to rotate around the sun. They might be distantly related to the Ancients, but they have their own natural circadian rhythm, their own feel for what is right, and thirty hour days are blatantly wrong. So much in the Pegasus galaxy doesn't feel right to them, without even considering the Wraith or semi-ascended beings or all the people who aren't what they appear to be.

Being uncomfortable is normal. Being a little bit grumpy because they never quite manage to fit into the pattern of life in a whole new galaxy is normal. Being too warm in what passes for winter on their new home is normal, as is the bickering between Rodney and Radek over the climate control settings.

*

It is Radek who first realizes that something is wrong, much to Rodney's dismay. Though in fairness Radek only stumbles across the matter – it isn't like it was a _genuine_ discovery, or anything. At least, that's what Rodney keeps telling everyone.

Radek isn't even doing anything serious; he's just playing (Rodney's term) with the capabilities of the Ancient computers. So the analysis he runs on changes in the city since they arrived isn't meant to show up anything important. He's simply curious as to how many statistical functions the system will run, how many of those he'll recognize, and how many he can adapt for other uses.

Radek's as good with figures as Rodney: he instantly sees patterns in numbers that someone else might take hours to spot. In this case, he doesn't need to be. A sixth grader would see the pattern. The numbers are increasing, and though it's not continuous, day-by-day, over the three years they've been in the city the increase is clear. Worse, it's exponential. And that's not meant to happen.

Sheppard is in the lab when Radek starts cursing. He stopped by to remind (remind, not nag, honestly) Radek about the two jumpers still awaiting repair. They're all used to the cursing, and most of them know a good selection of basic Czech swear words by now, but Sheppard can tell this is different.

*

When Radek brings the matter up in a meeting the next day, though, no one seems unduly perturbed.

"So, the city is getting hotter? That's easily fixed, isn't it?" Elizabeth asks with a smile.

"I'm not so sure—" Radek starts.

"We'll sort it," Rodney interrupts.

"Rodney, we do not know what is happening here."

"Yes, well, you might find it too much of a challenge, but I'm quite sure I can fix it."

"Could it be global warming?" Lorne suggests, and Radek and Rodney stop glaring at each other and laugh at Lorne instead.

"That's nonsense—"

"The city recycles perfectly—"

"And it's hardly as though the Athosians are pumping out greenhouse gases."

So that's that. There's no crisis, just a slightly odd matter resolved.

*

John doesn't forget though. He lies awake some nights, sheets thrown to the bottom of the bed because it's still a little too warm despite the altered environmental setttings, and listens. He listens to the city, and she sounds sad. When he gets up and leans against the wall, she shudders.

He doesn't tell anyone, naturally. After all, what would he say? That he listens to a wordless voice, that he pieces meaning out of the creaks and groans that you hear in any old building. He doesn't think there's anyone who would understand.

Besides, there's no real discernable difference in the way things function, nothing John can quantify, yet the city feels sluggish to him. Doors still open on command, transporters still get them from one side of the city to another in almost instantaneously and rooms light up as they always have. But John finds himself timing everything, and he thinks the city's reactions are getting slower.

Atlantis is old. They don't know how old, exactly, but they know it's a five figure number. Nothing is meant to last that long, but, somehow, the city has survived in its underwater bubble, waiting millennia for humans to arrive and bring her back to life.

But what if they're too late? What if she's sick, he thinks, and he's not sure where the idea comes from (it's crazy to think it's from Atlantis), but it takes root in his head and he can't get rid of it. He touches the city, sniffs the air, listens harder in the empty corridors, and he knows he's right.

*

He tells Rodney first, a casual _by the way_ on the return trip from a routine visit to the current Alpha site. He doesn't make a big deal out of it.

He expects Rodney to laugh at him.

Rodney doesn't.

Rodney asks questions, and John answers them as best he can, and then Rodney thinks for about two seconds, because that's all the time it takes him to piece it together.

"The city is sick," he announces, and John would put his heads in his hands and groan if he weren't flying the puddle jumper.

"Are you sure?" he asks, because he has to ask, even though he knows the answer.

"Yes."

"Can we cure it?"

"I don't know." And even though he's flying, John does close his eyes for a minute, wishing for a miracle or something, because this isn't just a building they're talking about. It's Atlantis. Home. More than just home, she's part of him, and he thinks she's been calling for help and he hasn't been answering.

*

Rodney explains what he thinks has happened. The city isn't a living entity, exactly, but it's closely attuned to the people living inside. And Atlantis was built for the Ancients. They had visitors, no doubt, back in the heyday of the city, but they would all have been natives of the Pegasus galaxy, and the city was used to them, designed for them.

But the expedition is from another galaxy, another era. Even so, they've managed to fit in, for the main. Their technology isn't meant to blend with technology that has been around for centuries, though it does, mostly, and apart from a few glitches they've managed to work with the old and new side by side. The problem doesn't lie with the technology. It lies with them. They're a new evolution of people, and carry a new evolution of disease, new genetic code.

Atlantis has tried to adjust to them, but their presence, their each and every touch, has infected her with material that she doesn't have the ability to deal with. Ever since Elizabeth – the first one – was swept back in time, the infection has been present. All the time the city was slumbering, waiting for the expedition to arrive (return), its progress was slow, barely noticeable. But when they came, so many of them with the gene that the city rejoiced and sprang into full wakefulness again, that's when it really started. When the infection began to creep through her.

Rodney theorizes that it's the AI that's most affected. And with that deteriorating, anything could happen.

The temperature rise is just a symptom, not the ailment. Rodney grumbles that he's not a doctor, and he's not supposed to be _diagnosing a city_ , but everyone understands that it's fear that's making him so ill-tempered. Fear of failure on such a huge scale. It's bad enough that he's destroyed half a solar system (a third, at most, he'll retaliate if anyone other than John says that). This is Atlantis, and failing here—

It's not acceptable.

*

It's almost funny how life goes on almost as normal, even after a discovery that's shaken them to the core. Oddly though, it's John who's still worrying most. He knows he's regarded as laid back, and sure, it's true, mostly. And not just because leaning is comfortable, or because drawling has always disconcerted his superior officers. He's good at making the best of things, but he can't see a good side to this.

A section of the science team, headed by Radek, is working on the problem. Rodney is working on it too, along with multiple other projects. And they give regular updates, even if it's only to say, couched in scientist-speak, that there's nothing new.

Elizabeth has a few more worry lines and smiles a little less often. But many of the expedition haven't been told about the issue – it's not deemed necessary – so they carry on, day to day, exploring the galaxy, avoiding the Wraith, searching for allies and ZPMs.

*

On P4X-227 they make a major discovery. They had worried for a while that the five gate addresses past-Elizabeth had given them might be the only ones where they had any chance of finding ZPMs. But they meet up with a group of nomadic traders – Teyla knows of them, from past trades with her people, and vouches for them – and the team learns of a planet that is rumored to be inhabited by ghosts. The traders aren't superstitious, and believe the ghosts might be - and here their vocabulary fails them, but John says holograms, and they say yes, holograms. Made by the gate builders, they think. They've been to the planet, and not seen the images themselves, but they believe that the Lanteans can wake the ghosts. John is impressed by their honesty, and he can see that Teyla is too, as she weighs them up.

It would make sense that the holograms would only be activated by those with the gene, so they take the suggestion of a trade back to Elizabeth. Rodney is bouncing on the balls of his feet, running through all the potential discoveries they might make – which vary from feasible to downright ludicrous - and John wants to go there too, and Elizabeth can see no harm in the idea, so she approves a trade.

They trade medicine for the gate address of the planet, Empurla, which they reference as P4X-227.

It's night when they arrive on Empurla, so Ronon and Teyla scout a reasonable perimeter while John puts up two tents and ignores all of Rodney's directions. John shares a tent with Rodney, and falls asleep to the sound of his snoring – it's almost as soothing as the ocean, he thinks, and smiles into his sleeping bag.

The sun is hot and harsh, even first thing in the morning, so they get ready to search for the Ancient technology as quickly as possible.

It's not hard to guess which direction they should go: there's a paved road leading in a straight line from the stargate. It's cracked but still serviceable, a dull red gash in the sepia of the surrounding dried out land.

"It's too obvious," Ronon mutters, hand hovering over his gun.

"Are you coming?" Rodney asks, ignoring Ronon, and doesn't wait for a response before heading out on the road.

It's not long before he's complaining though.

"It's far too hot."

"Surely it's lunchtime already? I can feel my blood sugar dropping, and I know I'm getting dehydrated too."

"Trust the American military to issue us with boots that don't fit well – why can't we just use the puddle jumper in stealth mode? Why do you always make us walk?" The last question is directed at Sheppard in a pitiful whine.

"You need the exercise," John tells him, inviting a spiel on just how fit Rodney is for a scientist whose brain is his most important asset. It serves to distract Rodney long enough for them to reach the end of the road, which was the whole idea.

The road comes to an end, not unexpectedly, at a group of ruins. Sandy, half-buried ruins that look like any other abandoned cities they've come across. Until they look closer, and see the shadows. Shadows which don't match up to the direction of the sun, and which move far too fast for shadows.

Ghosts, to the superstitious.

John raises his hand, silent, in a halt motion. He can see Rodney out of the corner of his eye, looking skittish.

"There could be snakes here," Rodney stage whispers, as though a few reptiles are something to be worried about when there are shadows that don't obey the laws of physics.

John moves slowly, carefully, towards the nearest building, P-90 at the ready.

Teyla and Ronon flank him on either side, but keep their distance, keeping watch outside the building.

As he walks through the remains of a doorway – the top of the arch is broken, and he's only guessing that there was once a door there – he senses something. A faint buzzing through his body, like the remnants of pins and needles or the static in a summer thunderstorm. And silence. He actually feels the silence, like a weight falling over him. He turns around, and he can see the others still, so he calls their names.

He sees Rodney mouthing, and raising his hands questioningly, but he can't hear a word, either directly or over the radio.

He shrugs. There's nothing he can do about it and no immediate danger in sight, so he carries on into a wide-open area, a meeting hall maybe, or something similar. There's a patch of moving shadow at the far side of the room, so he heads for it. It's not danger-lust, or anything crazy like that, despite the accusations Rodney has thrown at him after missions. It's just that the building has the aura of the Ancients still about it, if not the appearance, and John has a good feeling about this. Though he'll need to come up with something better than that for the mission report – Elizabeth tends to look disapprovingly at him when he goes by his gut feeling.

As he gets closer, he sees that the shadows aren't shadows, as such, more like black mist. It can't be actual mist, not in the heat of the sun that is already high in the sky. He pushes his P-90 in the shadow, watches the end of it fade away, then pulls it out. It's unharmed, so he sticks his hand in. And feels something hard, and smooth, but not with age, not like the ruins around him. It's smooth like metal, cold from the mist around it. He explores it with one hand, feeling something like a plinth supporting a low column, and, on top, a button.

He tilts his head to one side for a moment in thought. To press, or not to press.

There's really only one option.

He presses it.

The silence that he's just been getting accustomed to vanishes. A body rises up out of the mist, a man that looks almost as misty as his surroundings – John can see the wall though him – and starts to speak.

He speaks to John as though John is an Ancient – he must have recorded this before the Lanteans met Elizabeth and had any hope that anyone would venture here from Earth. He introduces himself as Rhan, the head of a team of engineers in the Atlantean military. His message is short and simple: he hopes the war with the Wraith is over, but, failing that, that the provisions stored on this planet for safe-keeping here will be of use to Atlantis in their fight.

He gives a set of figures – they sound like coordinates - and John writes them down quickly, hoping Rodney can make sense of them.

When Rhan has finished there is a soft explosion, and he vanishes, along with the strange mist and the blanket of silence surrounding the area.

Immediately there is a roar of sound in his ear: Rodney shouting, asking if he's okay, if he's dead.

"No, Rodney, I'm not dead."

"What was that explosion just then? Did you blow something up in there?"

"I don't always blow things up, you know," John replies. It's true – he'd rather shoot than blow things up. Less collateral damage.

"We are relieved to know that you are safe, Colonel Sheppard," Teyla tells him as he gets back to them, waiting outside the ruins.

John hands over his scribbled notes to Rodney, who mutters to himself for a few minutes, then tells them that they need to head due east to the other side of the ruins.

Rodney has clearly forgotten all thoughts of snakes or other dangers as he strides through the buildings. The shadows are all gone now, and the place is just like any other abandoned city – they could be on earth, if it weren't for the greenish tinge to the sky. He leads them straight to a large building, less damaged than the others, inside which they find a smaller building. Once they're inside that they find a small square chamber in the middle of the floor, cold to the touch like the metal stand. John pictures the building full of mist – the box wouldn't have been visible, even if anyone had braved the ghosts and gotten this far.

Ronon tries to lift the lid off, but he can't budge it, and even the combined efforts of all four of them can't do anything to move it. Until John strokes his hands over its surface, that is. Then there is an audible click, and John is able to lift the top off by himself.

Rodney and Teyla gasp, and even Ronon makes a pleased sound. It is far better than they could have possibly hoped. Not one ZPM, not two, but three.

"If these are fully charged—" Rodney says, and can't manage anymore. His hands are shaking as he reaches out for them, his eyes full of the sort of happiness John hasn't seen in them for a long time. It's the best sight John could imagine.

When John, Rodney, Ronon and Teyla come back through the gate, Rodney cradling a ZPM like his firstborn, there are loud cheers in the gate room.

When he reports that, although they've lost some charge, they all hold at least two-thirds of their original power, Colonel Caldwell produces a bottle of champagne from the Daedalus and tells them he's been saving it for this moment. They raise their glasses and call out their various versions of cheers, and there are smiles and laughter all around.

John thinks most of them have forgotten about Atlantis and her plight, at least for these few moments. But he hasn't, not even with the taste of not-bad-at-all champagne in his mouth, and the feel of Caldwell's slap on the back and Elizabeth's praise in his ears.

*

The smiles are all gone a few days later.

"Unscheduled offworld activation," comes the cry across the sound system.

John zips up – not even taking a leak is free from interruptions – and races to the gate room, just in time to see Dr. Beckett and a medic team lower a sheet over the body on the floor.

"Who?" Sheppard asks.

"Dr. Parrish," Lorne answers dully as he helps a limping Billick onto a stretcher.

John is alone, briefly, with Elizabeth before the post-mission debriefing, and he watches her pace the room.

"I thought it was a routine mission?" she says, almost angrily, although she knows almost as much about the mission as he does.

"Yeah, it was." And it had been, but this is the Pegasus galaxy, where even routine is dangerous. There's no reassurance he can give her.

Lorne arrives, then, a nurse at his side insisting that he must come to the infirmary immediately for a check up and that he's in no position to ignore her. Elizabeth waves him off, tells him the debriefing can wait, but he insists on giving her the basics at least, even though the blood from the gash above his eye is dripping onto the table, and his hands are shaking.

It wasn't Wraith or Genii, or any of the other dangers they've come to expect. It wasn't even wild animals. Just a planet with rock formations that looked more solid that they actually were. Dr. Parrish had been examining an unusual pattern of lichen growth when the cliff-face had started to crumble.

"He was so absorbed, he didn't even seem to notice us shouting at first," Lorne says, and sighs.

They don't need to hear much more – the results are obvious, Dr. Parrish dead, three others injured, and a planet that isn't as safe as they'd hoped.

*

They're used to deaths, of course, but the atmosphere is always quieter after one, especially someone as well liked as Dr. Parrish. Besides, it's one thing to be accustomed to something, it's another matter to learn to deal with it. Heightmeyer is always booked solid for the weeks following a loss, and there's less laughter, more awareness of their own mortality. There are more careless accidents too, as people sleep less, drink more. More arguments, even a fight between Ronon and a new marine who arrived with the latest batch on the Daedalus and was foolish enough to insult Teyla in Ronon's hearing.

It feels to John as though they're crumbling along with the city.

*

And one day, out of the blue, the city starts to fall. Literally.

John first hears of the problem over his headset. They still maintain regular patrols over as much of the city as possible, even while the Wraith threat isn't imminent. Normally they'll just report in to their section leader, who'll report to Sheppard or Lorne, whoever is currently on duty. So when the Sergeant covering the East pier calls in to Sheppard, he knows it must be something unusual.

It is.

The city has always looked pristine, almost new. Once they got rid of the dead plants littering the corridors, there had been nothing to show that the city was old.

But the Sergeant reports cracks in a walkway, and a section of pier that has just vanished, slid into the ocean.

When Sheppard gets there, it's as bad as it sounded. The walkway isn't safe, he can tell from a glance. The metal doesn't look shiny any more, but dull and matte, and the cracked edges are powdery. The pier is even worse – it looks as though more of it will go at any moment, so Sheppard immediately declares it out of bounds.

Before he heads back though, he squats down and runs one hand gently over the flaking rails and floor. He tries to tell himself it's purely to gather up some of the powdery material to take back with him for research, but he knows it's more than that. He wants to know if Atlantis is hurting, or, rather, how much she's hurting, because he knows without doubt that she's in pain. He can almost feel her shuddering under the light touch of his hand, and he wills comfort through the contact.

*

The team researching the city's sickness has fragmented – few of them are still involved in that research, other than as a side issue. The lack of progress, combined with the lack of noticeable problems made it seem less urgent, especially when there were always imminent dangers to worry about. They survived a meteor storm that lit up the city shields all through one night and left a giant crater frighteningly close to the Athosian settlement. And after that crisis there was another, and another, and even when they weren't fighting enemies or the elements there was no peace or rest. They suffered badly during the winter with a flu-like virus that they caught from a small planet that they'd visited to trade for food. The people who infected them were barely affected by it – no worse than a common cold – but the away team that came back soon ended up in the infirmary, feverish and vomiting. It wasn't a strain they'd come across before, and Carson had looked like a ghost of himself by the time it ran its course. Eleven people had died, and they'd had to cut the Athosians off from the gate for nearly a month to spare them the infection.

Two of those who died had been working on the Atlantis project, and they haven't been replaced, even though John knows Rodney has requested replacements. Carson worked on it for a while, but he's not had time all winter. So when John gets to the labs with the powder, he hands it over to Rodney, as he's the only one John knows for certain is still on the project. Rodney's already heard the news. He interrogates John about the pattern of cracks, the size of the damaged area, anything else he might have noticed, then dismisses him with a carelessly waved hand as he starts shouting for lackeys.

John doesn't see him again for days. And when he does, when Elizabeth orders Rodney out of the lab for the weekly briefing, John is shocked at the sight. Rodney's used to running on adrenaline and caffeine with a regular dose of sugar, and he's used to going long hours without sleep. But John has never seen him look this tired before.

*

The thing is, Rodney isn't supposed to say "can't". It's not meant to be part of his vocabulary. When he shakes his head and says, "I can't climb up there," on a mission, Sheppard will immediately show him that, actually, he can. And he does. And if he says, "I can't get this done in time," he always does manage, because there are almost always lives at stake, and Rodney has the ability to pull something extra out of the bag at the last moment. That's the kind of guy he is. The sort you want on your team. The sort you _need_ on your team, even if he drives you crazy half the time.

So Rodney has slowly stopped using the word. He says "maybe, because if anyone can, I can" instead of "can't", "I'll try if you'll just shut up and let me get on with it" instead of "it's impossible". It's been a long time since he said "can't".

Sheppard has come to rely on this, more even than he tells Rodney.

But Rodney can't go back in time and fix the problem, or grab a solution out of thin air like he's done a thousand times before. There are no schematics for Janus' time machine lying around, and not even Rodney has the knowledge to develop one. This time it really is too late, they've run out of time. Atlantis has run out of time.

And when Rodney tells Sheppard that in the next briefing – Rodney's addressing the entire room, but his eyes are fixed on Sheppard - John knows this is it. There's no misunderstanding the dismay in Rodney's eyes. He mutters the explanation, as if saying the words quietly will lessen the impact.

Sheppard finds a quiet Rodney one of the most terrifying things he's encountered in this galaxy. It makes him long to hear Rodney shout, or call someone an imbecile, or gesture so wildly that he knocks Dr. Zelenka's glasses off like he famously did during the debate about the value of P3X-419 as a potential mining operation. But Rodney's just saying "we can't do anything," and sitting back down at the table, shoulders hunched in defeat.

They're all quiet, and they all look crushed. Everyone is staring at the table, or into space, as though they can't bear to see the looks on each other's faces.

John shivers. It's crazy, shivering, when the city is running a fever and the office is full – every member of senior staff is here – and too hot. So he shouldn't be shivering. But he can't help it.

He has nothing to add, no plan to put in motion. There's no one to shoot or blow up, except maybe themselves, because they're the problem. They've done this, brought this on themselves, brought this on the city.

They're killing Atlantis.

And they don't know how to save her.

*

Elizabeth makes a city-wide announcement that evening.

"We have a serious situation," she begins. "As many of you will be aware by now, areas of the city are crumbling away. Dr. McKay and his team are working on the problem, and we hope that we will be able to find a solution soon. In the meantime, most of the city is to be regarded as off-limits, in the hope that we can limit the damage, and for everyone's safety. Your section leaders will provide you with a map showing the areas that we will be keeping in use."

Reactions are varied. Most have heard rumors, of varying accuracy, so the news isn't the surprise it might have been, though there are still some who are clearly shocked by the announcement. Sheppard comes across groups huddled together in agitated conversation that's broken off when he comes into view.

In practical terms, blocking off most of the city doesn't affect them greatly. There are still huge areas that they've not explored properly thanks to lack of time and manpower. They live and work almost entirely in one section anyway, grouped together near the operations tower for company as well as convenience.

Everyone is aware though. None as much as John, he suspects, but they're all aware. He sees it in their eyes when they walk down corridors looking for signs of aging. When they tread warily on stairs, or hesitate before entering a transporter. More people use stairs now, rather than trust the transporters, even though there haven't been any malfunctions.

John keeps his men busy with weapons drill and training, but he knows that most of them are visiting the labs in their spare time. They're feeling as helpless as he does. McKay waves him away impatiently whenever he stops by, unless he brings coffee or food. Then he'll stop for long enough to burn his mouth on the coffee, complain, then gulp it down anyway. He'll eat the food without looking up, working with one hand for a few minutes, practiced at juggling food and work. John's not sure if he ever goes back to his room to sleep any more.

*

Not everyone understands. John catches snippets of conversations, in the mess hall and the gym, in passing.

"It's like a computer virus, right?"

"Dunno. I suppose it must be."

"Can't we just unplug everything? Reboot the city systems like they did on the Daedalus?"

He doesn't bother to stop and put them right. He wishes it were as straightforward as a computer virus. If Atlantis were just a building, he's sure they'd have an answer by now.

But Atlantis is alive in subtle ways that they don't understand, and treating her is a whole new science that they don't even have a name for. She's not _truly_ sentient (at least not in ways they can measure), she's not organic, but she responds to them. John thinks she'll respond to them right to the end. He worries that she'll sacrifice herself for them, and he's not sure that the sacrifice will be worthwhile.

If Atlantis were just a building, she would be replaceable, they could rebuild her. But they're not gods, or even Ancients, and they can't recreate her, so if she dies—

Sheppard always pauses his thoughts there. He'd rather concentrate on practicalities, on what they can do, right now, rather than on what might happen.

They're going to have to make a decision soon. John capitalizes it in his head. The Decision.

He's started to make plans. Evacuation won't be difficult for those in the city – they have more than sufficient power to open the gate to return to Earth, even though they've sent one of their recent finds back to Earth. But they'll need a new home for the Athosians, so John makes it his private endeavor to find somewhere suitable for them. He's not ready to make the search official yet. No one has spoken of leaving, other than in the vaguest of terms – an 'if the worst happens' scenario. So he just scopes out planets that they visit, looks for somewhere safe and fertile and makes his own personal notes when he gets back to his room.

*

Messages go back and forth to Earth in even greater number than usual, and clearly someone there is worried, someone high up, because next time they open the gate to Earth for more than message transmission, Elizabeth goes through. She announces it in advance as a routine matter, but, privately, tells John that there are rumors spreading from Stargate Command, and she needs to set them straight.

"What sort of rumors?" he asks.

"You know, the usual kind of over the top reaction – someone must have mentioned the word virus," she says with a rueful smile. "Some want the expedition disbanded immediately, others want us to drop the research into the problem and focus on exploring the galaxy while the base is still viable."

"I see," he says, and that's that.

He's glad he's not going with her. Thinking of Atlantis in terms of a 'viable base' isn't something he can do these days. Not when he can sense her distress and pain. Atlantis has crept inside him, and he can't bring himself to care that he's become overly sentimental about her well-being.

Elizabeth returns a month later on the Daedalus. Her lips are pursed together as she disembarks, and she looks grim. She barely speaks to John beyond a passing greeting, but heads straight for the labs.

John follows.

She's brusque here too.

"Rodney, have you got anything for me?" she asks without preliminaries.

"We're working on a couple of theories, and it's possible that—"

"A solution, Rodney, is there a solution yet?" she interrupts.

Rodney looks as surprised as John feels. He shakes his head. "No, not yet."

"You've got ten days," she tells him, and walks off before he can begin to start spluttering out objections.

*

John gives her a couple of hours, and then goes in search of her. He finds her in the mess hall, sitting in the quietest corner, alone with a plate of salad that she's picking at uninterestedly.

"So, ten days, huh?" he says as he puts his tray down.

"It was the best I could get," she says, resignation battling anger in her tone.

"Why?" he asks, though he really wants to ask what happens after ten days. He reckons she'll tell him that though, in her own time.

"The government isn't a bottomless pit of money, or so they kept reminding us. They've read the reports and don't believe we can save Atlantis, so they feel the resources we're using on trying to 'prop up a crumbling edifice' (John hears the quotation marks in her voice) would be better spent battling enemies who are directly affecting Earth. They want us to rescue as much as we can, and take it back with us."

And leave the rest to fall in the sea. The words are unspoken, but they're clear.

"Rodney's got nothing yet." John's stew is tasteless but he takes another mouthful anyway.

"If he still doesn't have anything in ten days, then we start packing up."

"And Ronon, Teyla, the other Athosians?"

Elizabeth pauses with her fork in midair. John watches a piece of lettuce fall off the prongs.

"Ronon and Teyla can come back to Earth, if they wish. As for the others, we can find a suitable planet for them." She's cold efficiency now, brooking no argument. John thinks she probably wouldn't be able to cope with a debate, not right now.

He nods agreement, and attacks his stew. It's not that bad, really. Military food's no better on Earth.

*

On day four of the ten days allotted, John gets a wild message over his headset.

"I'm a genius. Well, obviously you knew that, but I'm even more of a genius. It's not just anyone that can work so far outside their own field you know, though technically it's fields plural, because I've always had well-rounded out scientific expertise—"

"Rodney?" John interjects, with what he feels is remarkable patience. "Are you trying to say you've found a solution?"

"Well of course that's what I'm saying. What else would I be saying?"

"I'll be right down."

He expects to hear celebrating as he nears the lab, but all he hears is babble. Inside, there's confusion. There are heads being shaken and people shouting and John has a bad feeling about it.

Rodney looks up as John walks in, almost as though he senses him.

"There were some errors in the theory," he says.

"Oh."

*

By day ten, there have been three more almost-solutions, and John has come running each time, only to find an argument between Rodney and Radek, or Rodney and Carson, or Rodney and whoever else Rodney has been particularly irritated by that day. There's a large digital clock in the corner of the lab, counting down the hours, minutes and seconds, and John thinks it would drive him crazy to have that in sight all the time.

Rodney shrugs when John asks about it.

"I like the pressure," he says, but John knows a lie when he hears one. There's nothing to like about this situation, and even the fact that the threat hanging over them is from Stargate Command, not the Wraith, doesn't make it any less bearable. Or less of a threat.

They'll walk out of here alive, of course, they have that virtual guarantee. They're not at risk of having the life sucked out of them, or of being trussed up and stored for a future meal. But they're a team, and Atlantis is part of that now, part of who they all are. She's protected them and their gift in return has been slow death and abandonment, and that's just not a fair deal.

John's seen a lot of injustice, often firsthand. He hates it. And now he hates that they're killing this amazing city and they've been given no time at all to save her. Most of all, though, he hates that he can't do anything about it, that he'll do his job, and that's it.

*

Most of the evacuation plans fall to John. Elizabeth agrees that it's best run as a military operation, so now it's his turn to stay up most of the night working. At least he's managed to do well by the Athosians – the thought of uprooting them again had rankled, but they find a working gate on a deserted planet and, with the help of the Daedalus, manage to relocate it to the Atlantis mainland. At least they still have a little luck on their side.

John's too busy even to notice that Ronon has packed up the assorted belongings he's acquired over the last couple of years. It's not until he offers to ferry Teyla to the mainland – he has to do it, even though he doesn't have time – that he learns that Ronon is going too. He feels like he's missed some signs, but he doesn't beat himself up about it. There's no point, and he's already got enough things to blame himself for.

Rodney claims that he needs to check the settings of the Athosian gate (again), so comes along too. One last journey together as a team.

The conversation is stilted and awkward, even worse than the first days of Ronon joining their team. John pretends he needs to concentrate on flying the jumper, even though he knows that won't fool any of them.

When they land, they stand grouped around the back of the jumper, bags and boxes piled to one side. Teyla bends her head, forehead to John's.

"Thank you for all you have done, for me and my people," she says simply, then turns and follows suit with Rodney.

Ronon grasps John by the hand.

"Good hunting, always." Ronon pauses, and John almost thinks that is it, that is goodbye, except for the gleam in Ronon's eye that says there is more to come. "When we're settled here, Teyla and I are to be joined."

"Congratulations." Rodney slaps Ronon on the back, holds out his hand to Teyla, and ends up awkwardly embracing her. It's the first time John has smiled in a while.

"We wish you could be with us for the ceremony," Teyla says softly.

"Yeah, me too," is all John can say, because they all know that's impossible, that once the expedition has gone they won't be returning.

*

"I need some of your men," Rodney says one morning when John bumps into him in the corridor.

John reverses direction and walks alongside Rodney. The pace is brisk; Rodney doesn't amble like he used to, doesn't even talk so much, as though there isn't time for such things anymore.

"How many?" he asks instinctively, then changes his mind. "No, wait, why do you want them?"

"I want teams to scour the city. There are far too many areas we haven't explored – there must be labs, libraries, weapons stores even that we should find before we leave. Just think of all the possibilities – it would be criminal to lose this chance to gather as much as we can to take back to Earth."

"Sorry, Rodney, but that's just not possible."

Rodney pauses in his tracks, looking astonished, before walking on even faster.

"What do you mean, not possible? You can spare a few men, surely."

"Not for that, no. And you're not to send any of the science team out unaccompanied either, not into any of the off limits areas."

"Why on earth not?" Rodney clearly hasn't even considered that John would refuse, and John hates doing this to Rodney, hates refusing him something he obviously desperately wants. But it's the right decision - or at least, it's the decision John has to make, which isn't necessarily exactly the same thing - so he tries to explain.

"Because the city's continuing to deteriorate – you know that – and it's not safe. I'm not willing to lose men, not on the off chance that they might, possibly, find something we can use."

"The risk's minimal – it's not like we can't see what areas are dangerous. We'll avoid anywhere that looks hazardous, and we'll still be able to check out a good sized area. I just need you to let me have a few teams. They can all be volunteers, if that makes you feel happier."

"The answer's still no, Rodney."

"Are you a total moron? Did you not hear me when I said what we might be losing? Precious data and knowledge that we'll never have another chance to discover, information that Earth needs to survive. There's not just the Wraith out there. There are the Ori and the Goa'uld, and no doubt other ghastly races we haven't come across yet who'll want to do even worse things than eat us alive or kill us if we don't worship them, and you can't possibly want us to lose the chance to learn enough to destroy them."

"I heard you, Rodney, but it doesn't change my answer."

"If you actually listened to what I said, how can you conceivably think it's not worth the risk?"

"Because I'm not fond of watching good people die. Are you?"

Rodney narrows his eyes, and John wonders for a second if Rodney is about to punch him. He almost wishes Rodney would, because then it might dispel the sick feeling John has inside him. Instead, Rodney about turns as sharply as any parade turn John has ever seen and marches off in the opposite direction.

John doesn't see Rodney again until the next day, and neither apologize, because neither of them said anything that they didn't mean, and they both know that. And they both know that Rodney thinks he's right, and that John thinks Rodney might be right but that John has to do his job. But Rodney doesn't move when John sits opposite him at dinner, and he pushes the salt towards John without being asked. It's enough.

*

"Do you still hear the city?" Rodney asks, out of the blue. They're crating up computers and consoles in the main lab, even John, because it's all hands on deck for the pack-up.

"I don't know," Sheppard answers truthfully. He still hears sounds that don't have any obvious origin, other than Atlantis, but they're faint and he doesn't sense anything beyond sadness. Overwhelming sadness. He's tried to tell the city that they're leaving, that maybe their leaving will help her, but he's not sure if she understands or not.

"Sometimes I think I do. Mostly at night. It always used to be so quiet and peaceful, just the sound of the sea, but now-- There are so many strange noises, and some of them almost sound like the city's trying to say something."

Rodney's quiet, almost reflective, but John isn't surprised. It's Atlantis that they're talking about, after all, and she doesn't leave people unaffected. None of them are going to be quite the same when they leave here.

*

Sheppard brings up the matter of Ford at the next main meeting – they're daily now, with so much to organize.

Elizabeth looks regretful.

"Do you have any ideas of where to start searching? Any clue that he might still be alive?" she asks.

"Well—No." John shrugs, looking around the table in the vain hope that someone, anyone, will suggest something. "But—"

"But nothing, Colonel. You know we can't spare man power on a wild goose chase, so unless you can persuade me that there's a real chance of finding him, I have to say no."

They move onto the next issue.

John lies awake a long time that night, trying to work out what he'll tell Ford's cousin and grandparents. He eventually falls asleep without an answer. He's been doing a lot of that lately.

*

The day they leave comes far too quickly. The Daedalus arrived the day before and is sitting in orbit above the city. It's like a vulture, waiting to pick over the bones, and John has to take a deep breath before speaking to Colonel Caldwell.

The atmosphere is subdued – the gate room is bustling with activity, but almost everyone is working quietly. Some of them haven't been home in months, years even, but there's no excitement.

John thinks he sees some blinked back tears as each person going through the gate looks back one last time. It's all sadly anticlimatic though – a few steps and they're gone, one by one, until only three of them are left. They're not going through the gate: they have the long journey home, on the Daedalus. And before they go, they have a job to do.

*

"I feel as though there should be some sense of déjà vu," Elizabeth comments as she and Rodney shroud work stations with the dust covers they'd found when they first arrived.

"At least this time we lasted years rather than hours." John finds a retractable pencil at the back of a console and slips it into a pocket – he doesn't want any trace of them left behind. "It wasn't a waste, the other you staying behind," he continues quietly so that only Elizabeth can hear. "I mean, you—she saved our lives, she gave us the chance to learn so much."

Elizabeth nods and places her hand on John's shoulder for a moment, whether in thanks or for her own reassurance he's not sure. And then they get back to the task of shutting down Atlantis.

(When John was ten, he'd had a dog for a while. They'd gotten her from the pound, so she'd already had a name, Vagabond, but he used to call her Ace.

She'd been put down a few months after they got her – she started vomiting one night, when John had snuck her into his room. She'd been sick all over his homework, and he was pissed off with her because he failed an assignment he'd spent hours on. He hadn't told anyone she'd been sick until days later when it happened again, only in front of his parents this time. Cancer. His dad hadn't pretended it was anything else, or that they could do anything to save her, because he believed in straight talk. John had gone to the vet's with his dad, and held her while they put her under. He hadn't cried until he got home, and even then he hadn't really cried, not much anyway, not so that it counted.)

He's dry-eyed now, but he feels as helpless and as absurdly negligent as he did then. As though he's missed something that might have saved her (saved Ace or saved Atlantis), something he should have noticed earlier.

He shakes his head quickly to clear his mind, and throws a cover over the nearest console. It's the last one in the room. They're finished.

"Should we say something before we go?" Rodney asks. "It seems odd just to leave."

"You know me, I'm not a speech-giving kinda guy."

Rodney and John both look at Elizabeth.

"I don't know," she demurs, then nods her head in acceptance. She looks around as she speaks, her farewell simple but formal. "Thank you, city of Atlantis, for all we've learned from you and from the people who created you. And to those whom we've lost and left behind, we say goodbye. Rest in peace."

They pause for a while, in the middle of the room. It's very quiet now, without even the faint hum of life that's always been present even in the middle of the night.

John clears his throat and activates his ear piece. "We're ready to come on board, sir."

*

"You do know exactly what you're doing, right? Because this isn't something we can afford to get wrong, and even though my calculations are perfectly correct, obviously, that's not going to help if you misapply them at this end."

John can't quite raise a smile, even at the look on Hermiod's face.

"Yes, Dr. McKay, I am fully aware of the importance of this task, but it is also perfectly within my capabilities. Perhaps you would like to join Dr. Weir on the bridge and _observe_?"

John notices Lieutenant Novak drop her head to hide her grin.

"I would rather _observe_ here."

Rodney's fingers are drumming on the console in front of him. He's never been good at standing by, so John takes it upon himself to distract him.

"How exactly are we going to destroy the gate?" he asks, even though he had been listening at the briefings when it was discussed, and he knows full well what's about to happen.

"Hermiod is going to beam it close enough to the sun for it to get pulled in. If he gets the coordinates right, which he should seeing as I sent him all the calculations and even he shouldn't be able to mess up his part of the task, it will start to disintigrate within five seconds of being beamed out of Atlantis. That way there'll be no doubt that it's been destroyed. We don't want to have to worry about some hive ship finding it and getting a free trip to Earth."

"We're ready now." Novak turns back to Hermiod, who presses a single button.

John can hear Rodney counting under his breath. _One, two, three, four, five._

"It is done," Hermiod says.

Rather an anticlimax, John thinks, no explosion to see or hear, just a dot on a screen flickering and then disappearing.

"Colonel Sheppard, Dr. McKay, you might want to look down at the city." Elizabeth's voice sounds shocked through his headset, so John grabs Rodney by the arm and they run to an observation window.

The city is sinking. The piers (those still remaining) are already almost under water, and even as they watch they disappear.

Rodney's mouth drops in an _oh_ of surprise. "I guess that's really it then."

They watch until there's nothing left to see but an expanding ring of ripples. They're so high up the swells look like no more than the trace left when a pebble lands in a pond, but they must be miles wide by the time they too vanish.

John grips the rail in front of him and says his own, silent, goodbye to the city that was so much more than just a home.

*

John doesn't have plans after the weeks of debriefing at SGC and the awkward goodbyes with the civilians on the expedition are finally over – he's done enough planning for a while. So when General Landry tells him to take some vacation time (an order, not a suggestion), and Rodney says he's rented a car and Sheppard should join him, John goes along with it.

They cross four states in two easy stages, John driving and Rodney providing the commentary. Even at twenty miles above the speed limit, it feels leisurely. They've no immediate time restrictions, no place they have to be, no danger beyond Rodney's close encounter with a snake-shaped stick at a roadside pit stop. John considers suggesting they stop at Reno, but his foot stays on the gas, and they keep on Route 80. They stop for food and gas a couple of times, loading up on Twinkies and Oreos and chips that Rodney munches noisily and shares begrudgingly. Rodney refuses to travel through the night so they share a shabby room at a roadside motel and argue over the remote until they both fall asleep to the sound of some late night movie neither of them were really watching.

Rodney's rented a house too. It's on the bluff at Bodega Harbor, just off Highway 1. They get there at midday, just as the sun is burning off the last of the ocean fog, and the cool breeze is a welcome respite from the inland heat.

But now John's standing on the balcony looking out over the Pacific, he wishes he'd thought a bit more, made some plans of his own. He could have visited his buddy Clay – he's got a small ranch down in Argentina, and there's a ski resort less than a day's drive away. He could have gone any of a million places that didn't have the sound of the ocean.

Rodney joins him, handing over a cold beer, and swigging from a bottle himself.

"Good stuff," he says.

John checks the label. It's not great, but it goes down well, and any real beer is still a luxury.

"Yeah, good stuff."

"You haven't mentioned Atlantis once since we left SGC. If you want to talk about it—" Rodney trails off, but John appreciates the gesture.

"Not really," John says, but he thinks he might once he's had a few more beers.

"It was a close call, huh? Getting off just before the city sank." Rodney's on his third beer now, and he never was much good at recognizing a conversation stopper.

"She didn't sink."

Rodney looks baffled. "Sheppard, we saw it happen. You saw it too."

"No, Rodney, she didn't sink. She submerged."

"She— _Oh_." Rodney's fast, as always, even with a couple of beers inside him. "It's possible that she'll be able to heal herself, without—"

"Without us. Yeah."

"Does anyone else know?"

John shakes his head. "No." He hasn't told anyone else. Besides, he has no proof, just gut instinct that tells him that the city retreated to save herself, that she waited until they were all gone so she could begin to heal. No one else is going to believe him.

Just Rodney. They're the only two people in the universe who know that Atlantis might still survive, deep under the ocean. Waiting.

*

The first two nights on earth he dreamed of Atlantis. Dreamed that she was getting hotter and hotter and everyone was burning up inside her and he was ordered to leave them and he did. He left them all to burn. He woke up sweating and had to tell himself that he'd never do that, no matter what, but he couldn't get rid of the image.

The third night he dreamed that the ocean was boiling and the fish were dead and it was all his fault. After that he got some pills from Dr. Lam - who handed them over with a shrewd glance but didn't say anything - and even if it was still his fault, at least he didn't dream about it.

The first night in Bodega Harbor he doesn't dream at all. He doesn't sleep either – he just sits on the balcony cradling the last beer in one hand, the other arm numb where Rodney's fallen asleep against him, drooling slightly from his half-open mouth. He hears the soft rumble of the Pacific ocean, and listens to Rodney snoring, and thinks that maybe, just maybe, he can live with this.


End file.
